But you're missing some key facts here.
First - that 1996 team was ranked #5. No way no how does a #5 team get left out of BCS/NY6/whatever game in this day and age, even if that #5 team has one loss.
Second - that 2001 team was told they were not under consideration for a BCS/NY6/whatever game when they were 12-0 and top 10 in the country. Sure - when Staley went down the wheels came off (and I'd accept an argument that with the defense displayed at Hawaii, having Staley wouldn't have mattered).
So - I see where you're coming from. And I'd even argue that Utah (and BSU) have played well and deserved what they've gotten. But I don't think it's a stretch to say that some of the reaction to BYU being left out of the BCS predecessors played a role in other G5 teams gaining access.